GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

Platforms:

GPL162 GPL10463

21 Samples

Download data: CEL, PAIR

(Submitter supplied) In this study, we performed expression profiling experiments to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and compared the global gene expression profiles.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL162

15 Samples

Download data: CEL

(Submitter supplied) In this study, we performed a ChIP-chip experiment to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and immuno-precipitated the regions of the genomic DNA interacting with the sigma factors.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10463

6 Samples

Download data: PAIR

(Submitter supplied) In Rhodobacter sphaeroides a transcriptional response to the reactive oxygen species singlet oxygen is controlled by the group IV sigma factor RpoE and the anti-sigma factor ChrR. In this study, we integrated various large datasets to identify genes within the singlet oxygen stress response that contain RpoE-dependent promoters within R. sphaeroides. Transcript pattern clustering and a RpoE-binding sequence model were used to predict candidate promoters that respond to singlet oxygen stress in R. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10463

6 Samples

Download data: GFF, TXT

(Submitter supplied) Oligo probes are 45bp in average, tiling the genome sequences with about 35-bp overlap between consecutive probes. Every other probe hybridizes to the reverse strand. Native array description file: 2007-06-20_R_sphaeroides_long85_v2.ndf Native array description file: 2007-06-20_R_sphaeroides_long85_v2.pos Protocol: See manufacturer's web site (www.nimblegen.com)

Organism:

Cereibacter sphaeroides 2.4.1

4 Series

21 Samples

Download data: NDF, POS

(Submitter supplied) Vibrio cholerae, the cause of cholera, can grow in a variety of environments outside of human hosts. During infection, the pathogen must adapt to significant environmental alterations, including the elevated temperature of the human gastrointestinal tract. σ32, an alternative sigma factor encoded by rpoH, activates transcription of genes involved in the heat-shock response in several bacterial species. more...

Organism:

Vibrio cholerae; Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by array

Platform:

GPL3651

6 Samples

Download data: TXT

(Submitter supplied) Sinorhizobium meliloti can live as a soil saprophyte, and can engage in a nitrogen fixing symbiosis with plant roots. To succeed in such diverse environments, the bacteria must continually adjust gene expression. Transcriptional plasticity in eubacteria is often mediated by alternative sigma factors interacting with core RNA polymerase. The S. meliloti genome encodes 14 of these alternative sigmas, including two putative RpoH (heat shock) sigmas. more...

Organism:

Medicago truncatula; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL9757

27 Samples

Download data: CEL

(Submitter supplied) Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Cultures with low aeration, which underwent strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures, which showed little variation in levels of dissolved oxygen. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17213

8 Samples

Download data: WIG

(Submitter supplied) Investigation of whole genome gene expression level changes in a Sinorhizobium meliloti 1021 rpoH1 rpoH2 double mutant, compared to the wild-type strain. The mutations engineered into this strain render it deficient in symbiotic nitrogen fixation. The mutants analyzed in this study are further described in Mitsui, H, T. Sato, Y. Sato, and K. Minamisawa. 2004. Sinorhizobium meliloti RpoH1 is required for effective nitrogen-fixing symbiosis with alfalfa. more...

Organism:

Sinorhizobium meliloti 1021

Type:

Expression profiling by array

Platform:

GPL19375

20 Samples

Download data: CALLS, PAIR

(Submitter supplied) The bacterial heat-shock response is regulated by the alternative sigma factor sigma 32 (RpoH), which responds to misfolded protein stress and directs the RNA polymerase to the promoterss for genes required for protein refolding or degradation. In P. aeruginosa, RpoH is essential for viability under laboratory growth conditions. Here, we used a transcriptomics approach to identify the genes of the RpoH regulon, including RpoH-regulated genes that are essential for P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

6 Samples

Download data: CEL

(Submitter supplied) Comparing wild type to strain lacking anti sigma factor ChrR. Aerobic conditions (30% oxygen). Keywords = SigmaE Keywords = ChrR Keywords = Oxygen stress Keywords: other

Organism:

Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Dataset:

GDS1106

Platform:

GPL162

2 Samples

Download data: CEL, RPT

Expression profiling of anti-sigma factor ChrR deletion mutant grown aerobically in 30% oxygen. Binding of ChrR to sigma(E) blocks sigma(E)-dependent transcription.

Organism:

Rhodobacter sphaeroides; Rhodobacter sphaeroides 2.4.1

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL162

Series:

GSE2219

2 Samples

Download data: CEL, RPT

(Submitter supplied) In previously published work, we identified three Mycobacterium tuberculosis sigma (s) factor genes responding to heat shock (sigB, sigE and sigH ). Two of them (sigB and sigE ) also responded to SDS exposure. As these responses to stress suggested that the s factors encoded by these genes could be involved in pathogenicity, we are studying their role in physiology and virulence. In this work, we characterize a sigE mutant of M. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL2787

15 Samples

Download data: TXT

(Submitter supplied) DNA microarray analysis of genes regulated by the alternative sigma factor, sigma 32 (rpoH). Sigma 32-dependent genes were initially identified by comparing a wild type (wt) E. coli K-12 strain that has a low level of sigma 32, with a strain over-expressing sigma 32 (following induction of rpoH from an inducible promoter by IPTG). We monitored changes in gene expression in 4 separate time-courses. Because sigma 32 is negatively regulated, its activity decreases 10 min after overexpression. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Dataset:

GDS1804

Platform:

GPL3500

16 Samples

Download data

Expression profiling of cells at various time points up to 10 minutes following induction by IPTG of alternative sigma factor, sigma32, from an inducible promoter. Sigma32 mediates the heat shock response. Results identify genes regulated by sigma32.

Organism:

Escherichia coli

Type:

Expression profiling by array, log2 ratio, 2 agent, 5 time sets

Platform:

GPL3500

Series:

GSE4321

16 Samples

Download data

(Submitter supplied) This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

8 Samples

Download data

(Submitter supplied) Naturally occurring mtrR mutants of gonococci displaying clinically relevant levels of antibiotic resistance are often isolated from patients and mtrR mutants have been reported to be more fit than the wild type parent strain in a murine vaginal infection model. DNA-binding proteins, such as MtrR, that negatively regulate bacterial efflux pump genes have been considered to be “local” gene regulators, although there is increasing evidence that they can directly or indirectly influence expression of other genes. more...

Organism:

Neisseria gonorrhoeae

Type:

Expression profiling by array

Platform:

GPL7218

6 Samples

Download data: CEL, TXT

(Submitter supplied) To learn more about the function of SorX, we constructed an over-expression strain. For this purpose, the sorX gene together with its 28-bp upstream region was cloned into the over-expression vector pRK4352 and expressed in the R. sphaeroides wild-type 2.4.1 background. The corresponding strain consequently exhibits a SorX over-expression that is driven by the constitutive 16S rRNA (RSP_4352) promoter. more...

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL15457

3 Samples

Download data: TXT

(Submitter supplied) Effect of hsf1-R206S/F256S mutation on heat-induced transcription of genes is analyzed. Total RNA was isolated from HSF1 wild type and hsf1-R206S/F256S cells grown at 39oC for 15 min. Probe cDNA was primed by oligo(dT) and was synthesized in the presence of 33P-dCTP. Hybridization was carried out using the same GF100 GeneFilter. Value higher than 30 in HSF1 wild type cells is confident. Values from duplicate experiments were averaged, and the average fold changes were calculated. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS1073

Platform:

GPL205

4 Samples

Download data

Analysis of a heat shock transcription factor 1 (HSF1) temperature sensitive mutant strain subjected to heat stress at 33 degrees C. HSF1 mutant contains an arginine to serine and a phenylalanine to serine substitution at residues 206 and 256 respectively. Results identify novel targets of HSF1.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, transformed count, 2 genotype/variation sets

Platform:

GPL205

Series:

GSE2103

4 Samples

Download data